update deps and test for reading some witsml entities (#17)

* update deps and test for reading some witsml entities * new verification taking car of WITSML sub element (AbstractObject inside Other AbstractObject like ChannelSet in Log) + new REST API for epc/xml validation and correction * README * readme * bugfix in creation object selection with package name in web interface
geosiris-technologies · Dec 22, 2023 · a86aaff · a86aaff
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diff --git a/README.md b/README.md
@@ -40,6 +40,13 @@ The WebStudio is a web application that allows to manipulate energyml file (such
     - 3D visu : 
         - *ColorInformation* in a *GraphicalInformationSet* can be used if it references an **HSV color** in a *DiscreteColorMap*
 
+- 1.0.14:
+    - REST API : 
+        - A REST API has been added to be able to validate/fix EPC/xml files.
+    - Bugfix : 
+      - Sometimes export the EPC file was failing from the interface. It was due to specific entities that were not supported for export.
+      - Witsml/Prodml objects (like **Log**) can contain as *sub-objects* other *AbstractObject*. They are now detected during validation/auto-correction.
+
 ## License
 
 This project is licensed under the Apache 2.0 License - see the `LICENSE` file for details
@@ -184,3 +191,27 @@ Change the **docker/server-production.xml** to have a connector like this:
     </SSLHostConfig>
 </Connector>
 ```
+
+## REST API
+
+The WebStudio provides a simple REST API to validate and correct EPC/xml files.
+
+### Validation : "/EnergymlValidation"
+
+A post request on the endpoint "/EnergymlValidation" with files inside "form-data" will return a json file containing information about the correctness of your xml/epc files.
+
+The messages help you with a dotted notation for each error. Example : *".ChanelSet.O.Channel.1"* means the 2nd Channel xml element in the 1st sub xml element "ChannelSet".
+
+Example with postman : 
+![POSTMAN-validation-request](doc/image/REST/postman-energyml-validation.png)
+
+### Correction : "/EnergymlFix"
+
+A post request on the endpoint "/EnergymlFix" with files inside "form-data" will return an EPC file containing all of your xml files (even taken from an input EPC file), and also a log file that describes the modifications done to correct your entities.
+
+For now the only correction done is on DOR information. If an object refers to an other one with its UUID, the *Title* and the *QualifiedType*/*ContentType* are verified and eventually fixed.
+
+**Export version:** The resulting EPC can follow the old file naming convention "/[ENERGYML_TYPE]\_[UUID].xml" but also the new one : "/[PACKAGE][PACKAGE\_VERSION]/[ENERGYML\_TYPE]_[UUID].xml". The new version is obtainable by sending a parameter called "version" with the value **EXPANDED** (uppercase).
+
+Example with postman : 
+![POSTMAN-correction-request](doc/image/REST/postman-energyml-fix.png)
diff --git a/doc/image/REST/postman-energyml-fix.png b/doc/image/REST/postman-energyml-fix.png
diff --git a/doc/image/REST/postman-energyml-validation.png b/doc/image/REST/postman-energyml-validation.png
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <groupId>com.geosiris</groupId>
     <artifactId>webstudio</artifactId>
     <name>${project.groupId}:${project.artifactId}</name>
-    <version>1.0.12</version>
+    <version>1.0.14</version>
     <organization>
         <name>Geosiris</name>
         <url>http://www.geosiris.com</url>
@@ -63,7 +63,7 @@
         <dependency>
             <groupId>com.geosiris</groupId>
             <artifactId>energyml-utils</artifactId>
-            <version>1.0.7</version>
+            <version>1.0.9</version>
         </dependency>
         <dependency>
             <groupId>com.geosiris</groupId>
@@ -135,6 +135,19 @@
             <artifactId>jol-core</artifactId>
             <version>0.10</version>
         </dependency>
+        <!-- Tests -->
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+            <version>5.9.1</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <version>5.9.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
     <build/>
     <profiles>
@@ -178,5 +191,18 @@
                 </plugins>
             </build>
         </profile>
+        <profile>
+            <id>test</id>
+            <build>
+                <plugins>
+                    <!-- Tests -->
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-surefire-plugin</artifactId>
+                        <version>2.22.2</version>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
     </profiles>
 </project>
diff --git a/src/main/java/com/geosiris/webstudio/model/WorkspaceContent.java b/src/main/java/com/geosiris/webstudio/model/WorkspaceContent.java
@@ -65,10 +65,16 @@ public void setAdditionalInformation(Map<String, Object> additionalInformation)
     }
 
     public void putAll(WorkspaceContent rf) {
-        this.notReadObjects.addAll(rf.notReadObjects);
-        this.readObjects.putAll(rf.readObjects);
-        this.additionalInformation.putAll(rf.additionalInformation);
-        this.parsedRels.putAll(rf.parsedRels);
+        if(rf != null){
+            if(rf.notReadObjects != null)
+                this.notReadObjects.addAll(rf.notReadObjects);
+            if(rf.readObjects != null)
+                this.readObjects.putAll(rf.readObjects);
+            if(rf.additionalInformation != null)
+                this.additionalInformation.putAll(rf.additionalInformation);
+            if(rf.parsedRels != null)
+                this.parsedRels.putAll(rf.parsedRels);
+        }
     }
 
     public Map<String, Relationships> getParsedRels() {

diff --git a/src/main/java/com/geosiris/webstudio/servlet/ExportEPCFile.java b/src/main/java/com/geosiris/webstudio/servlet/ExportEPCFile.java
@@ -15,10 +15,9 @@
 */
 package com.geosiris.webstudio.servlet;
 
-import com.geosiris.energyml.utils.EPCGenericManager;
 import com.geosiris.energyml.utils.ExportVersion;
-import com.geosiris.energyml.utils.Pair;
 import com.geosiris.webstudio.model.WorkspaceContent;
+import com.geosiris.webstudio.utils.HttpSender;
 import com.geosiris.webstudio.utils.SessionUtility;
 import jakarta.servlet.ServletContext;
 import jakarta.servlet.ServletException;
@@ -30,16 +29,12 @@
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
-import java.io.ByteArrayOutputStream;
 import java.io.IOException;
-import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipOutputStream;
 
 /**
  * Servlet implementation class ExportEPCFile
@@ -103,46 +98,14 @@ protected void doGet(HttpServletRequest request, HttpServletResponse response) t
             }
             // FIN filtrage fichiers a exporter
 
-            try {
-                ByteArrayOutputStream bos = new ByteArrayOutputStream();
-                exportEPCFile(bos,
-                        workspace,
-                        exportVersion);
-                byte[] bos_bytes = bos.toByteArray();
+            request.setAttribute("response", "File exported");
 
-                request.setAttribute("response", "File exported");
+            // obtains ServletContext
+            ServletContext context = getServletContext();
 
-                // obtains ServletContext
-                ServletContext context = getServletContext();
-
-                // gets MIME type of the file
-                String mimeType = context.getMimeType(filePath);
-                if (mimeType == null) {
-                    // set to binary type if MIME mapping not found
-                    mimeType = "application/octet-stream";
-                }
-
-                response.setContentType(mimeType);
-//                response.setContentLength((int) downloadFile.length());
-                response.setContentLength(bos_bytes.length);
-
-                // forces download
-                String headerKey = "Content-Disposition";
-                String headerValue = String.format("attachment; filename=\"%s\"", filePath);
-                response.setHeader(headerKey, headerValue);
-
-                // obtains response's output stream
-                OutputStream outStream = response.getOutputStream();
-
-                for(int chunk=0; chunk<bos_bytes.length; chunk+= 4096){
-                    outStream.write(bos_bytes, chunk, Math.min(4096, bos_bytes.length-chunk));
-                }
-
-                outStream.close();
-            } catch (Exception e) {
-                logger.error(e.getMessage(), e);
-                request.setAttribute("response", "Error occured while exporting file : \n" + e.getMessage() + " \n " + Arrays.toString(e.getStackTrace()));
-            }
+            // gets MIME type of the file
+            String mimeType = context.getMimeType(filePath);
+            HttpSender.writeEpcAsRequestResponse(response, workspace, filePath, exportVersion, mimeType);
 
             String closeEpc = request.getParameter("close");
             if (closeEpc != null && closeEpc.toLowerCase().compareTo("true") == 0) {
@@ -162,41 +125,4 @@ protected void doPost(HttpServletRequest request, HttpServletResponse response)
         doGet(request, response);
     }
 
-    public static void exportEPCFile(OutputStream out,
-                                     WorkspaceContent workspace,
-                                     ExportVersion exportVersion){
-        logger.info("@exportEPCFile");
-        try {
-            try(ZipOutputStream epc = new ZipOutputStream(out)) {
-                for (Map.Entry<String, Object> kv : workspace.getReadObjects().entrySet()) {
-                    ZipEntry ze_resqml = new ZipEntry(EPCGenericManager.genPathInEPC(kv.getValue(), exportVersion));
-                    epc.putNextEntry(ze_resqml);
-                    Editor.pkgManager.marshal(kv.getValue(), epc);
-                    epc.closeEntry();
-                }
-                EPCGenericManager.exportRels(workspace.getReadObjects(), workspace.getParsedRels(), exportVersion, epc, "Geosiris Resqml WebStudio");
-
-                if (workspace.getNotReadObjects() != null) {
-                    /// non resqml obj
-                    for (Pair<String, byte[]> nonResqmlObj : workspace.getNotReadObjects()) {
-                        ZipEntry ze_resqml = new ZipEntry(nonResqmlObj.l());
-                        epc.putNextEntry(ze_resqml);
-                        try {
-                            byte[] fileContent = nonResqmlObj.r();
-                            for(int chunk=0; chunk<fileContent.length; chunk += 4096){
-                                epc.write(fileContent, chunk, Math.min(4096, fileContent.length-chunk));
-                            }
-                        } catch (Exception e) {
-                            logger.error(e.getMessage(), e);
-                            logger.error("nonResqmlObj " + nonResqmlObj.l());
-                        }
-                        epc.closeEntry();
-                    }
-                }
-//                epc.finish();
-            }
-        } catch (IOException e) {
-            logger.error(e.getMessage(), e);
-        }
-    }
 }